Classifications

• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
  • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6813—Hybridisation assays
  • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
  • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips

Definitions

• Methicillin-resistant Staphylococcus aureus (MRSA) strains contain a SCCmec cassette, which may contain the mecA gene whose gene product confers methicillin resistance.
• SCCmec cassette Specific detection of MRSA by the presence of the SCCmec cassette has been used in a number of publications and patents (U.S. Pat. No. 6,156,507, US 2005019893). These various methods all rely on the use of primer set(s) where one (or more) primers target the S. aureus chromosomal DNA (external to SCCmec) and the other one (or more) primers target the SCCmec cassettes near the chromosomal integration site.
• SCCmec cassettes are also found in other Staphylococcus species, commonly known as coagulase-negative staphylococci, including S. epidermidis, S. hominis, S. haemolyticus and others. Current methods therefore use primers directed specifically to S. aureus chromosomal DNA (non-cassette regions) to assess the species identification and to avoid confusion between SCCmec cassettes detected in S. aureus and those in other staphylococci.
• Oligonucleotides or oligonucleotide mimics as defined herein can be used in methods to detect MRSA and MRCNS and to distinguish MRSA from MRCNS.
• the oligonucleotides and oligonucleotide mimics are, in some embodiments, set forth in the tables herein, and comprise sequences SEQ ID NOs 1-36.
• the oligonucleotides and oligonucleotide mimics are generally referred to as probes, especially as used in hybridization methods, or as primers, especially as used in DNA amplification methods.
• the invention is a method of testing a sample for the presence or absence of SCCmec cassette DNA present as an insertion in chromosomal DNA of Staphylococcus aureus .
• the method includes (a) hybridizing the sample, under appropriate conditions, to one or more capture probe(s) that hybridize to chromosomal DNA of Staphylococcus aureus external to SCCmec by at least partially complementary sequences, the capture probe(s) being optionally attached to a support, (b) hybridizing the sample to one or more detector probe(s) that hybridize to SCCmec cassette DNA by at least partially complementary sequences, and (c) detecting each of the detector probe(s), which may include application of means of detection appropriate to the probe (and not all probes may be detected) thereby determining that the SCCmec cassette DNA is present and that it is integrated into the chromosomal DNA of Staphylococcus aureus .
• the hybridizations (a) and (b) can be carried out at the same time or can be carried out in either order.
• the sample to be tested can be hybridized to one or more blocker probe(s) that hybridize to DNA of one or more other species of staphylococci as part of step (a).
• Another method tests a sample for the presence of DNA of S. aureus comprising SCCmec.
• the method includes performing an amplification reaction using the sample as a source of template DNA.
• a first primer comprises a nucleobase sequence complementary to a nucleobase sequence within SCCmec of at least one SCCmec type of Staphylococcus species.
• a second primer hybridizes to chromosomal DNA of S. aureus external to SCCmec.
• the results of the amplification reaction are analyzed for the presence of amplification product. If the amplification product is present, DNA of S. aureus comprising SCCmec is present in the sample.
• kits with components to carry out the assay methods.
• the kits include oligonucleotide or oligonucleotide mimics to be used as probes or primers, as appropriate to the method, and can include other reagents and solutions.
• a solid support may be supplied with capture probe attached, or for attachment of capture probes, for example.
• S. aureus -specific probes near the integration site for the SCCmec cassette is complicated by the high degree of sequence similarity between the chromosomal DNA of Staphylococcus species, (herein, the term “chromosomal DNA” is limited to regions external to any SCCmec, if present) which may explain false-positive results by current methods (Francois, et al., J Clin Microbiol. 45(6):2011-2013, 2007).
• improved specificity is possible using blocker probes that prevent hybridization of S. aureus -specific probes to other Staphylococcus species.
• Another parameter complicating probe design is sequence heterogeneity of chromosomal DNA between S. aureus strains within the S. aureus -specific target regions, such that a single probe does not hybridize to all S. aureus strains as shown in Example 3. This may be overcome by simply designing multiple probes as also shown in Example 3, but this invention offers the advantage of designing fewer probes, or even a single probe directed towards a non- S. aureus -specific region which, when used in conjunction with blocker probes as shown in Example 6, eliminates hybridization to other Staphylococcus species.
• the invention includes oligonucleotides and oligonucleotide mimics, including those comprising the nucleobase sequences described herein, and including those consisting of the nucleobase sequences described herein.
• Probes and primers comprising oligonucleotides or oligonucleotide mimics are part of the invention and are suitable for the assays described herein.
• Oligonucleotide mimics include, for example, phosphorothioate oligonucleotides, peptide nucleic acids (PNAs), and locked nucleic acids (LNAs).
• Oligonucleotide mimic portions and oligonucleotide portions can be combined in one chimeric oligonucleotide (e.g., a PNA/DNA chimera or a LNA/DNA chimera). Such chimeric oligonucleotides are also included within “oligonucleotide mimics.” Like oligonucleotides that may be found naturally occurring in cells, oligonucleotide mimics are spoken of as having a nucleobase sequence according to the A, C, G, T and U base portion of each of their respective monomer units.
• oligonucleotide mimics can form hybrids through Watson-Crick basepairing with DNA and/or RNA comprising a nucleobase sequence that is at least partially complementary.
• the oligonucleotides may be isolated.
• An oligonucleotide or oligonucleotide mimic can be provided as (in solution for example) the only probe, or it can be provided as a combination of one or more probes.
• probes are presented which bind to conserved regions of nucleic acid targets, though with some mismatched bases. As described herein, probes were designed that can form hybrids with these regions even though many of the bases in the probe are mismatched.
• the probe design is based on an “average” sequence from the alignment of several sequences derived from nature. The probe incorporates bases at each position which are complimentary to at least one of the natural sequences. The resulting probe is partially complimentary to all of the sequences it was designed against.
• the design method is similar to the well known concept of degenerate probes (primers), where a given probe sequence is designed with “wobble” bases incorporated, such that the final probe produced is actually composed of a population of two or more distinct sequences based on a general core sequence. This design method is different from degenerate probes in that there is only one probe sequence based on consensus complementarities. This type of generic mismatching probe is referred to as a “consensus” probe herein.
• Consensus probes can be used in combination with blocker probes.
• Blocker probes are well defined in the art and at their simplest can be defined as probes which bind specifically to nucleic acid targets which are not targets of interest. Very often blocker probes are designed such that they can not be detected. Blocker probes are used as part of a probe cocktail to prevent evolution of detectable signal from targets which are not of interest. Blocker probes and consensus probes together, as described herein, can be used to prevent signal evolution from specific nucleic acid targets.
• blocker probes and consensus probes offer the advantage of utilizing sequence differences outside the target/non-target region, such that only a part of the blocker probe(s) is used to reduce binding of the consensus probe to the non-target sequence.
• the use of one and two blocker probes utilizing sequence differences is exemplified in Example 5 and 6. This aspect of the invention is not limited to the sample or assay type but is a general concept providing improved specificity for nucleic acid analysis, and can be viewed as a means of using a longer target sequence.
• Another aspect of this invention is the use of very short probes which facilitates design of probes outside target regions with sequence heterogeneity.
• Very short probes are therefore not perceived by prior art in nucleic acid detection methods where high specificity is required, and in fact were specifically ruled out by earlier practitioners as being untenable for detection of SCCmec cassettes in S. aureus (US 2005019893).
• This invention is exemplified for the detection of MRSA but is equally suitable for detection of MRCNS and in fact offers the potential for using the same probe set(s) comprising consensus probe(s) and probe(s) for SCCmec for detection of the SCCmec cassette in staphylococci (with differentiation between MRSA and MRCNS (methicillin-resistant coagulase negative)) and supplemented with either blocking probes preventing hybridization of the consensus probe to non- S. aureus staphylococci for detection of MRSA, or blocking probes preventing hybridization of the consensus probe to S. aureus for detection of MRCNS.
• the invention comprises probes for the detection of SCCmec in S. aureus ; see Examples 1, 2 and 3.
• the probes comprise less than 15 nucleobases and are oligonucleotide mimics comprising LNA or PNA, detecting one or more SCCmec types (see Examples 4 and 5) and may be used in combination to detect multiple SCCmec types (see Example 4 and Example 5).
• the invention comprises a method for detecting SCCmec in S. aureus using the probes in combination with one or more probes hybridizing to chromosomal DNA of S. aureus .
• These may be either hybridizing specifically to S. aureus only (Example 6) or to other species of Staphylococci (Example 7).
• blocker probes may be included to prevent hybridization of the probe(s) to other Staphylococcus species (Examples 7 and 8).
• step a) hybridizing the sample to one or more capture probes and step b) (hybridizing the sample to one or more detector probes) can occur by combining the appropriate reagents in sequence, or can occur by combining the appropriate reagents in one hybridization mixture so that hybridizing steps a) and b) occur at the same time.
• the method to detect SCCmec in S. aureus in a sample may include lysing the cells in the sample, denaturing the DNA in the sample, incubating the DNA with one or more capture probes hybridizing to SCCmec types and one or more probes hybridizing to S. aureus chromosomal DNA. Protocols to carry out sandwich-type DNA hybridization assays or target amplification assays are known in the art.
• Kits comprising probe set(s) and optionally also comprising reagents are also a part of the invention. Instructions to use the kit can also be a component of the kit. DNA control standards can also be included.
• Capture probes can be supplied attached to a support, such as in the wells of a microtiter plate. One capture probe can be supplied in a set of wells, or more than one capture probe can be supplied together in the same wells. Detector probes can be provided individually packaged, or more than one detector probe can be packaged together. Blocker probes, if included in the kit, can be provided individually packaged, or more than one blocker probe can be packaged together. Blocker probes can be included with detector probes.
• probes of the sequences of capture probes can be used in assays as detector probes and vice versa, so long as the appropriate probes are used together in the assay.
• This invention is exemplified using sandwich hybridization but is also applicable to other hybridization methods and to nucleic acid amplification techniques.
• DNA amplification methods can be used to detect MRSA in a sample, as these methods, in effect, detect a nucleobase sequence internal to SCCmec, and a nucleobase sequence on the S. aureus chromosome external to SCCmec on a template DNA of S. aureus present in the sample.
• the amplification methods can use as primers any of the oligonucleotides or oligonucleotide mimics described as probes herein, or can use shorter portions of those molecules.
• Primers of a variety of lengths, comprising PNA or LNA can be used, e.g., primers of 14, 13, 12 11, 10 or fewer monomers.
• the primers can comprise the nucleobase sequences described for any of the oligonucleotides or oligonucleotide mimics described herein as capture probes or detector probes, so that a primer pair for amplification consists of one oligonucleotide or oligonucleotide mimic with the nucleobase sequence of a capture probe and one oligonucleotide or oligonucleotide mimic with the nucleobase sequence of a detector probe.
• LNA/DNA primers comprising both LNA and DNA monomers
• LNA/DNA primers shorter than DNA primers of the same sequence can be used successfully to amplify DNA by the polymerase chain reaction.
• LNA/DNA primers as short as 10 monomer units resulted in amplified product.
• the detection of MRSA by sandwich hybridization methods and by amplification methods such as the methods shown herein exemplifies a more general method that can be applied to the detection of other DNA or RNA targets (e.g., a gene for virulence in pathogenic bacteria, an allele associated with a genetic disease in humans, or a sequence indicating a mutation, a chromosomal rearrangement, deletion or insertion).
• DNA or RNA targets e.g., a gene for virulence in pathogenic bacteria, an allele associated with a genetic disease in humans, or a sequence indicating a mutation, a chromosomal rearrangement, deletion or insertion.
• the use of short LNA or LNA/DNA oligonucleotide mimics as probes or primers as demonstrated herein can be generally applied to the detection of other target DNAs in other assays.
• Oligonucleotide mimics comprising LNA can be substituted for oligonucleotides of the same nucleobase sequence for use as primers or probes, with greater sensitivity in assays.
• the length of an effective probe or primer can be shorter in an oligonucleotide mimic comprising LNA, compared to an oligonucleotide.
• hybridize or “hybridizing” means the sequence specific binding of any of two single stranded nucleic acids or oligonucleotides or oligonucleotide mimics to form duplexes according to Watson-Crick base-pairing rules.
• Hybrids may form between two nucleobase sequences which are not perfectly complementary as defined by the W-C base pairing rules, but are substantially complimentary such that they form stable double stranded complexes under assay conditions, also referred to as partially complementary consensus probes.
• a sample to be used in the assays described herein can be, for example, bacteria from one or more isolated colonies, or bacteria grown in a liquid or other culture, either isolated or mixed. Additionally, a sample can be bodily fluid or washings as might be obtained for analysis in a clinical laboratory, or an aliquot of such fluid or washings.
• Staphylococcus species is used to indicate any of the species of staphyloccocci.
• EVIGENE a sandwich-type DNA hybridization assay (Skov et al., Journal of Antimicrobial Chemotherapy 43: 467-475, 1999; Levi and Towner, J. Clin. Microbiol. 38: 830-838, 2003) to specifically detect genetic markers in staphylococci.
• EVIGENE kit components AdvancedDx, Woburn, Mass.
• generic assay products were used for all experiments differing only by the individual probes as listed in the Examples below. For each sample, 2 drops of Lysis I solution were added to 2 mL microcentrifuge tubes with lockable lids.
• the resulting mixture comprised NaCl, Tris and detergent as known to facilitate hybridization of the probes to the bacterial nucleic acid.
• the well was covered with plate sealing tape and placed in a microtiter plate shaker/incubator set at 55° C. and 400 rpm and incubated for 60 min. After incubation, the well was emptied and 2 drops of Conjugate Buffer were added, followed by 1 drop of Conjugate. The well was covered with plate sealing tape and incubated at 35-37° C. for 30 min. After the end of incubation, the well was then emptied, washed 4 times with 7 drops (or 4 ⁇ 200 ⁇ l) of Wash Solution.
• a variety of bacteria strains from AdvanDx A/S, Denmark were used. The identity (species and type, if available) of each isolate was based on information available from the supplier of the strains and/or other tests, such as EVIGENE tests for detection of mecA (gene for methicillin resistance) and nuc ( S. aureus -specific gene).
• DNA probes and probes comprising LNA nucleobases were obtained from TAG Copenhagen A/S (Copenhagen, Denmark). Capture probes were labeled for immobilization onto microtiter wells and Detector probes were labeled for detection via colorimetric signal amplification using components from commercial EVIGENE kits (AdvanDx). Blocker probes were unlabeled.
• Table 1.1 displays the nucleobase sequences of the Capture and Detector probes used in the experiment.
• the Capture probe targets the S. aureus DNA and has 10 mismatches to Staphylococcus epidermidis DNA.
• the Detector probe targets SCCmec types I, II, and IV (not III and V).
• Samples were prepared and assayed essentially according to the EVIGENETM procedure using Capture probe GenCP2 (60 nM) and Detector Probe Dt1 (5 nM).
• the mecA result of each isolate (using the MRSA EVIGENETM kits) as well as the MRSA results according to the invention, i.e. specific detection of mecA in S. aureus by detection of the SCCmec cassette in S. aureus only, are shown in Table 1.2.
• the final column displays the absorbance readings at 492 nm. Absorbance readings above background levels indicate the presence of the nucleic acid target in the sample.
• sandwich hybridization such as EVIGENE
• EVIGENE is a suitable assay format and is thus an alternative to PCR for specific detection of SCCmec in S. aureus.
• Table 2.1 displays the nucleobase sequences of the Capture and Detector probes used in the experiment.
• Capture probe GenCP2 (the same as in Example 1).
• Detector probe Dt1 (designed to be specific for SCCmec type I, II & IV),
• Detector probe Type III (designed to be specific for SCCmec type III)
• Detector probe Type V (designed to specific for SCCmec type V, Table 2.1).
• Samples were prepared and assayed essentially according to the EVIGENETM procedure using Capture probe GenCP2 (60 nM) and Detector Probe Dt1 (5 nM). Detector Probe Type III (5 nM), or Detector Probe Type V (5 nM).
• Table 3.1 displays the nucleobase sequences of the Capture and Detector probes used in the experiment. Additional detector probes were tested based on sequences in WO02099034.
• Samples were prepared and assayed essentially according to the EVIGENETM procedure using Capture probe GenCP2 (60 nM) and Detector probe Dt1 (5 nM) and Detector probe Type III (5 nM), or Detector probe Type V (5 nM), Detector probe Type5 (5 nM), Detector probe Type4 (5 nM), Detector probe Type7 (5 nM), Detector probe type 6 (5 nM), or Detector probe type 8,9 (5 nM).
• the Capture probe GenCP3 was tested together with Detector probe Dt1, Type III, and Type V (5 nM each) or with Detector probe Type5 (5 nM), Detector probe Type4 (5 nM), Detector probe Type7 (5 nM), Detector probe type 6 (5 nM), or Detector probe type 8,9 (5 nM).
• Example 3 show that the strains which did not test positive with GenCp2 and the detector probes described in Example 2 (Dt1, Type III & Type V) tested positive when alternate detector probes or another capture probe (GenCp3) was included in the test.
• the data show that multiple Capture and Detector probes may improve sensitivity and that additional probes may be added as additional “false-negative” strains (new SCCmec types) occur.
• Table 4.1 displays the nucleobase sequences of the Capture and Detector probes used in the experiment.
• Samples were prepared and assayed essentially according to the EVIGENETM procedure using the Detector probe Dt1(5 nM), 9-mer Dt5 LNA/DNA (50 nM) or 9-mer DNA (50 nM) and Capture probe GenCp3 (60 nM) above (Table 4.1).
• Results of Example 4 are summarized in Table 4.2, which displays the absorbance values obtained at 492 nm and the positive/negative results for the samples.
• the experiment showed that only the methicillin-resistant S. aureus strains of SCCmec type I, II or IV were positive (OD 492 >0.5) using the Capture GenCp3 and a 40-mer DNA or a LNA/DNA 9-mer Detector Probe, whereas a 9-mer DNA Detector Probe with the same sequence as the LNA/DNA gave a negative result when testing the same samples.
• Table 5.1 displays the nucleobase sequences of the Capture and Detector probes used in the experiment.
• the 9-mer PNA Detector Probe Dt10 was designed to detect SCCmec type I, II and IV.
• Probe Type Name Sequence (5′ to 3′) Capture GenCP2 AATCCTTCGGAAGATAGCATCTTTCCTTGTAT TTCTAATG (SEQ ID NO: 1) Detector T1, 2, 4- ctgcggagg Dt 10 (SEQ ID NO: 13) PNA monomers are lowercase a, g, c, t, and DNA monomers are uppercase A, G, C, T Method
• Samples were prepared and assayed essentially according to the EVIGENETM procedure using the Detector probe 9-mer Dt10 PNA (50 nM) and Capture probe GenCp2 (60 nM) above (Table 5.1).
• Results of Example 5 are summarized in Table 5.2, which displays the absorbance values obtained at 492 nm and the positive/negative results for the samples.
• the experiment showed that only the methicillin-resistant S. aureus strains of SCCmec type I, II or IV were positive (OD 492 >0.5) using the Capture GenCp2 and PNA 9-mer Detector Probe (Dt10).
• the data also show that replacing some of the naturally occurring nucleotides with non-naturally-occurring PNA monomers allows for the use of short probes.
• Table 6.1 displays the nucleobase sequences of the Capture and Detector probes used in the experiment.
• Capture probe (GenCp3, Table 4.1), all the SCCmec Detector probes (Dt1, type III, type V, Type5, Type4, Type7, type 6 and type 8,9, Table 3.1) and Blocker probes (B4A and B4B or the B5, Table 6.1) were used.
• Samples were prepared and assayed essentially according to the EVIGENETM procedure using the Detector probes (5 nM each) and Capture probe GenCp3 (60 nM) above with and without the Blocker probes (50 nM each).
• Results of Example 6 are summarized in Table 6.2, which displays the absorbance values obtained at 492 nm and the positive/negative results for the samples.
• Capture GeneCp3
• SCCmec Detector Probes all methicillin-resistant S. aureus strains (all SCCmec types) were positive as well as methicillin-resistant S. warneri.
• Blocker probes designed to hybridize to chromosomal DNA of S. warneri (not S. aureus )
• specific detection of methicillin-resistant S. aureus was obtained.
• the Blocker probes thus effectively prevent the Capture probe from hybridizing to chromosomal DNA of S. warneri , thereby allowing for specific detection of methicillin-resistant S. aureus.
• Table 7.1 displays the nucleobase sequences of the Capture (GenCp4) and Detector probe (Dt) and Blocker probes (B1A and BIB) used in the experiment below.
• the Capture probe is designed to hybridize to chromosomal DNA of S. aureus and S. epidermidis .
• the Detector probe is designed to hybridize to SCCmec type I, II & IV (not III and V) and the Blocker probes are designed to hybridize to chromosomal DNA of S. epidermidis (not S. aureus ).
• Samples were prepared and assayed essentially according to the EVIGENETM procedure using the Detector (5 nM) and Capture probes (60 nM) above with and without the Blocker probes (50 nM each).
• Results of Example 7 are summarized in Table 7.2, which displays the absorbance values obtained at 492 nm and the positive/negative results for the samples. Absorbance readings (OD 492 >0.5) above background levels indicate the presence of the nucleic acid target in the sample.
• the methicillin-resistant S. epidermidis and methicillin-resistant S. aureus strains of SCCmec type I, II or IV were all positive (OD 492 >0.5) using the Capture and Detector Probe, whereas only the methicillin-resistant S. aureus strains were positive when using Blocker probes.
• the Blocker probes thus effectively prevent the Capture probe from hybridizing to chromosomal DNA of S. epidermidis , thereby allowing for specific detection of methicillin-resistant S. aureus without using a S. aureus -specific capture probe.
• This aspect of the invention provides an advantage over previous design schemes as the location of the probe is less limited.
• Table 8.1 displays the nucleobase sequences of the Capture (GenCp4) and the Blocker probes (B1A and BIB) from Example 7, combined with the Detector probe (Dt5) from Example 4.
• Samples were prepared and assayed essentially according to the EVIGENETM procedure using the Detector (Dt5, 50 nM) and Capture probe (GenCp4, 60 nM) above with and without the Blocker probes (B1A and BIB, 500 nM each).
• Example 8 Results of Example 8 are summarized in Table 8.2, which displays the absorbance values obtained at 492 nm and the positive/negative results for the samples. Absorbance readings (OD 492 >0.5) above background levels indicate the presence of the nucleic acid target in the sample.
• This example shows that the Blocker probes prevent the Capture probe from hybridizing to chromosomal DNA of S. epidermidis , thereby allowing for specific detection of methicillin-resistant S. aureus without using a S. aureus -specific capture probe.
• the results also showed that mecA-positive S. aureus strains of SCCmec type I, II or IV tested positive with a 9-mer Detector probe hybridized together with the S. epidermidis Blocker probes.
• Table 9.1 displays the nucleobase sequences of the Capture probe GenCp3 with the Detector probe Dt5 (from Examples 4 and 8), Dt12 and Dt1.
• Probe Type Name Sequence (5′ to 3′) Capture GenCP3 TGTTCAATTAACACAACCCGCATCATTTG ATGTGGGAATG (SEQ ID NO: 5) Detector Dt1 GCTATTATTTACTTGAAATGAAAGACTGC GGAGGCTAACT (SEQ ID NO: 2) Detector T1, 2, 4-Dt5 GaggctaaC (SEQ ID NO: 11) Detector T1, 2, 4-Dt12 gaggctaac (SEQ ID NO: 20) LNA monomers are lowercase a, g, c, t, and DNA monomers are uppercase A, G, C, T Method
• Samples were prepared and assayed essentially according to the EVIGENETM procedure using the Detector probe Dt1(5 nM), 9-mer Dt5 LNA (50 nM) or 9-mer LNA (50 nM) with Capture probe GenCp3 (60 nM) above (Table 9.1).
• Example 9 Results of Example 9 are summarized in Table 9.2, which displays the absorbance values obtained at 492 nm and the positive/negative results for the samples.
• the experiment showed that the methicillin-resistant S. aureus strains of SCCmec type I, II or IV were positive (OD 492 >0.5) using the Capture GenCp3 with a 40-mer DNA or 9-mer mixed LNA/DNA Dt5 or a 9-mer only LNA (Dt12) Detector Probe.
• Table 10.1 displays the nucleobase sequences of the Capture probe (GenCp3) and the Detector probes Type III and Type III-Dt2.
• Samples were prepared and assayed essentially according to the EVIGENETM procedure using the Detector probe Type III (5 nM) and 9-mer Type III-Dt2 LNA/DNA probe (50 nM) and Capture probe GenCp3 (60 nM) above (Table 10.1).
• Example 10 Species ADx ID Type Type III-Dt2 OD 492 Type III OD 492 Staphylococcus #303 SCCmec type Positive 1.732 Positive 1.693 aureus III Staphylococcus #301 SCCmec type Positive 1.676 Positive 1.704 aureus IIIa Staphylococcus #352 MR-CNS Negative 0.214 Negative 0.117 epidermidis Staphylococcus #156 MSSA Negative 0.273 Negative 0.158 aureus
• Example 10 Results of Example 10 are summarized in Table 10.2, which displays the absorbance values obtained at 492 nm and the positive/negative results for the samples.
• the experiment showed that the methicillin-resistant S. aureus strains of SCCmec type III were positive (OD 492 >0.5) using Capture probe GenCp3 and a 40-mer DNA or 9-mer mixed LNA/DNA Detector Probe.
• Table 11.1 displays the nucleobase sequences of the Capture (GenCp3) with the Detector probes Type V and Type V-Dt4.
• Probe Type Name Sequence (5′ to 3′) Capture GenCP3 TGTTCAATTAACACAACCCGCATCATTTGATGTG GGAATG (SEQ ID NO: 5) Detector Type V ACTTTAGTCAAATCATCTTCACTAGTGTAATTAT CGAATG (SEQ ID NO: 4) Detector Type V- accattcac Dt4 (SEQ ID NO: 22) LNA monomers are lowercase a, g, c, t, and DNA monomers are uppercase A, G, C, T Method
• Samples were prepared and assayed essentially according to the EVIGENETM procedure using the Detector probe Type V (5 nM) and 9-mer Type V-Dt4 LNA probe (50 nM) and Capture probe GenCp3 (60 nM) above (Table 10.1).
• Example 11 Results of Example 11 are summarized in Table 11.2, which displays the absorbance values obtained at 492 nm and the positive/negative results for the samples.
• the experiment showed that the methicillin-resistant S. aureus strain of SCCmec type V was positive (OD 492 >0.5) using the Capture GenCp3 and a 40-mer DNA or 9-mer LNA only Detector Probe.
• MSSA is methicillin sensitive Staphylococcus aureus.
• Table 12.1 displays the nucleobase sequences of the PCR primers with specific LNA substitutions used in the PCR experiment below.
• the primers are designed to hybridize to genomic DNA of S. aureus or to a SCCmec type II as found in S. aureus strain Mu50.
• the DNA template was genomic bacterial DNA (Mu50, ATCC 700699), isolated with DNeasy Blood & Tissue kit (Qiagen). All DNA and LNA primers were suspended in 10 mM Tris. PCR amplification was performed in 50 ⁇ L reactions using 1 of each PCR primer, 800 ng or 8 ng genomic DNA and AccuPrime Taq DNA polymerase with AccuPrime buffer II, and 10 mM dNTPs (Invitrogen). Thermal cycling began with denaturation at 94.0° C. for 3 min followed by 30 cycles of 94.0° C. for 30 s, 55.0° C. for 30 s and 68.0° C. for 30 s. PCR product was visualized on 2% agarose gels with ethidium bromide and a 100 bp DNA ladder (Invitrogen). Images of the gels were taken with a digital camera.
• the forward Dt-F1 (SEQ ID NO:2) primer has the same sequence as Detector probe Dt1 used in the previous experiments.
• the primer pairs are listed in Table 12.2. Eight different primer pairs were tested for amplification of 800 ng (undiluted) or 8 ng (1:100) genomic DNA.
• Forward and reverse primer sequences are listed in Table 12.1.
• the primer pairs are listed in Table 12.3.
• Gel C eight different primer pairs were tested for amplification of 800 ng (undiluted) DNA. All amplicons (200 bp) were made with a forward Dt1-F5 (13-mer LNA/DNA primer) or Dt-F5-DNA (13-mer DNA primer), paired with GenCP3-R3 (14-mer LNA/DNA primer) or GenCP3-R7 (12-mer LNA/DNA) as reverse primers.
• Gel D four different primer pairs were tested for amplification of 800 ng (undiluted) DNA (Gel D, Table 12.3).
• All amplicons (200 bp) were made with a forward Dt1-F15 (11-mer LNA/DNA) primer or Dt-F11-DNA (11-mer DNA) primer, and GenCP3-R3 (14-mer LNA/DNA), reverse primer.
• Gel E four different primer pairs were tested for amplification of 800 ng (undiluted) DNA (Gel D, Table 12.3).
• All amplicons (200 bp) were made with a forward Dt1-F16 (10-mer LNA/DNA) primer or Dt-F16-DNA (10-mer DNA) primer, and GenCP3-R3 (14-mer LNA/DNA) reverse primer.
• the experiment showed that the methicillin-resistant S. aureus strain Mu50 of SCCmec type II was detected by PCR by using a 13-, 11- or a 10-mer forward LNA/DNA and a 14- or a 12-mer reverse LNA/DNA primer, but not detected by PCR when using DNA-only primers with the same sequence and length.

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